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        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.25

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-07, 09:50 CET based on data in: /DKHC/scratch/markop/_p_Endophytes/_I_Bsubtilis/_S_NGS_mixed_cultures_exp2/_A_03_exp2-STAR_limma/output


        General Statistics

        Showing 0/60 rows and 3/7 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedTrimmed bases
        BS830
        21.8M
        19.9M
        91.0%
        18.9M
        86.7%
        0.9M
        BS830_1
        0.5%
        BS830_2
        0.6%
        BS831
        22.2M
        20.6M
        92.5%
        19.7M
        88.3%
        0.9M
        BS831_1
        0.5%
        BS831_2
        0.6%
        BS832
        21.3M
        19.4M
        91.1%
        18.6M
        87.1%
        0.9M
        BS832_1
        0.5%
        BS832_2
        0.6%
        BS833
        20.6M
        18.9M
        91.8%
        18.1M
        88.0%
        0.8M
        BS833_1
        0.5%
        BS833_2
        0.6%
        BS839
        24.2M
        21.4M
        88.6%
        20.3M
        83.8%
        1.2M
        BS839_1
        0.6%
        BS839_2
        0.6%
        BS840
        20.3M
        17.3M
        84.9%
        16.2M
        79.9%
        1.0M
        BS840_1
        0.5%
        BS840_2
        0.5%
        BS847
        25.7M
        19.9M
        77.3%
        18.2M
        70.5%
        1.7M
        BS847_1
        0.5%
        BS847_2
        0.5%
        BS848
        21.4M
        19.4M
        90.5%
        18.5M
        86.6%
        0.8M
        BS848_1
        0.5%
        BS848_2
        0.5%
        BS849
        21.4M
        15.7M
        73.2%
        14.9M
        69.4%
        0.8M
        BS849_1
        0.8%
        BS849_2
        0.5%
        BS855
        20.4M
        17.3M
        85.0%
        16.4M
        80.6%
        0.9M
        BS855_1
        0.5%
        BS855_2
        0.5%
        BS856
        21.6M
        19.6M
        91.1%
        18.8M
        87.3%
        0.8M
        BS856_1
        0.4%
        BS856_2
        0.5%
        BS857
        21.2M
        19.0M
        89.5%
        18.1M
        85.3%
        0.9M
        BS857_1
        0.5%
        BS857_2
        0.5%
        BS862
        23.2M
        21.0M
        90.5%
        20.2M
        86.9%
        0.8M
        BS862_1
        0.5%
        BS862_2
        0.5%
        BS863
        22.6M
        18.9M
        83.6%
        17.7M
        78.3%
        1.2M
        BS863_1
        0.5%
        BS863_2
        0.5%
        BS864
        24.7M
        17.9M
        72.5%
        17.0M
        68.7%
        0.9M
        BS864_1
        0.8%
        BS864_2
        0.8%
        BS865
        38.6M
        34.2M
        88.7%
        32.8M
        85.0%
        1.4M
        BS865_1
        0.5%
        BS865_2
        0.5%
        BS870
        20.2M
        18.2M
        90.3%
        17.4M
        86.2%
        0.8M
        BS870_1
        0.5%
        BS870_2
        0.5%
        BS871
        25.3M
        16.1M
        63.7%
        15.3M
        60.5%
        0.8M
        BS871_1
        0.5%
        BS871_2
        0.5%
        BS872
        25.5M
        22.2M
        86.9%
        21.2M
        82.9%
        1.0M
        BS872_1
        0.5%
        BS872_2
        0.5%
        BS873
        21.8M
        18.7M
        86.0%
        17.8M
        81.5%
        1.0M
        BS873_1
        0.5%
        BS873_2
        0.5%

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 0/20 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        BS830
        21.8M
        19.9M
        91.0%
        18.9M
        86.7%
        0.9M
        298.0bp
        291.7bp
        18.4M
        16.6M
        18.2M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.0%
        3.2bp
        BS831
        22.2M
        20.6M
        92.5%
        19.7M
        88.3%
        0.9M
        298.0bp
        291.3bp
        18.6M
        16.7M
        18.3M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        3.2bp
        BS832
        21.3M
        19.4M
        91.1%
        18.6M
        87.1%
        0.9M
        298.0bp
        291.6bp
        18.4M
        16.6M
        18.2M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.0%
        3.2bp
        BS833
        20.6M
        18.9M
        91.8%
        18.1M
        88.0%
        0.8M
        298.0bp
        291.2bp
        17.3M
        15.6M
        17.1M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        3.2bp
        BS839
        24.2M
        21.4M
        88.6%
        20.3M
        83.8%
        1.2M
        298.0bp
        290.3bp
        16.7M
        14.9M
        16.5M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS840
        20.3M
        17.3M
        84.9%
        16.2M
        79.9%
        1.0M
        298.0bp
        290.1bp
        12.4M
        11.0M
        12.3M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.7bp
        BS847
        25.7M
        19.9M
        77.3%
        18.2M
        70.5%
        1.7M
        298.0bp
        290.6bp
        14.5M
        12.9M
        14.4M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.4bp
        0.1%
        3.7bp
        BS848
        21.4M
        19.4M
        90.5%
        18.5M
        86.6%
        0.8M
        298.0bp
        291.0bp
        16.5M
        14.7M
        16.3M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.4bp
        BS849
        21.4M
        15.7M
        73.2%
        14.9M
        69.4%
        0.8M
        298.0bp
        291.2bp
        13.3M
        11.9M
        13.1M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.4bp
        BS855
        20.4M
        17.3M
        85.0%
        16.4M
        80.6%
        0.9M
        298.0bp
        290.2bp
        12.8M
        11.4M
        12.6M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS856
        21.6M
        19.6M
        91.1%
        18.8M
        87.3%
        0.8M
        298.0bp
        290.3bp
        15.6M
        13.9M
        15.4M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS857
        21.2M
        19.0M
        89.5%
        18.1M
        85.3%
        0.9M
        298.0bp
        290.2bp
        14.4M
        12.9M
        14.2M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS862
        23.2M
        21.0M
        90.5%
        20.2M
        86.9%
        0.8M
        298.0bp
        290.5bp
        16.5M
        14.8M
        16.3M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS863
        22.6M
        18.9M
        83.6%
        17.7M
        78.3%
        1.2M
        298.0bp
        290.5bp
        14.8M
        13.2M
        14.6M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS864
        24.7M
        17.9M
        72.5%
        17.0M
        68.7%
        0.9M
        297.0bp
        289.4bp
        12.6M
        11.2M
        12.5M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.6bp
        BS865
        38.6M
        34.2M
        88.7%
        32.8M
        85.0%
        1.4M
        298.0bp
        290.7bp
        29.8M
        26.7M
        29.4M
        0.3M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.3bp
        BS870
        20.2M
        18.2M
        90.3%
        17.4M
        86.2%
        0.8M
        298.0bp
        290.5bp
        14.0M
        12.5M
        13.9M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.5bp
        BS871
        25.3M
        16.1M
        63.7%
        15.3M
        60.5%
        0.8M
        298.0bp
        290.5bp
        12.7M
        11.4M
        12.5M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.4bp
        0.1%
        3.7bp
        BS872
        25.5M
        22.2M
        86.9%
        21.2M
        82.9%
        1.0M
        298.0bp
        290.6bp
        18.0M
        16.2M
        17.8M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.4bp
        0.1%
        3.5bp
        BS873
        21.8M
        18.7M
        86.0%
        17.8M
        81.5%
        1.0M
        298.0bp
        290.6bp
        14.3M
        12.9M
        14.2M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.6bp

        Alignment Scores

        Created with MultiQC

        Gene Counts

        Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

        Created with MultiQC

        Cutadapt

        Version: 2.10

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Cutadapt2.10